BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971306.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 7,237,735 number of mapped reads = 6,170,217 (85.25%) number of secondary alignments = 0 number of mapped bases = 242,551,190 bp number of sequenced bases = 242,526,949 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 346,737 duplication rate = 4.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 35.4393 >>>>>>> ACTG content number of A's = 68,739,483 bp (28.34%) number of C's = 50,865,257 bp (20.97%) number of T's = 70,749,005 bp (29.17%) number of G's = 52,159,627 bp (21.51%) number of N's = 13,577 bp (0.01%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 848,520 number of insertions = 10,043 mapped reads with insertion percentage = 0.16% number of deletions = 19,936 mapped reads with deletion percentage = 0.32% homopolymer indels = 37.27% >>>>>>> Coverage mean coverageData = 0.0784X std coverageData = 0.666X There is a 6.52% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 19143894 0.07680580262225305 1.2075450361488473 chr2 243199373 20001211 0.08224203357629545 0.625773683809421 chr3 198022430 16305863 0.08234351532803633 0.33568136416180244 chr4 191154276 16236826 0.0849409510462638 0.39485548461159053 chr5 180915260 14963119 0.08270788765967006 0.343368833731989 chr6 171115067 13959993 0.08158248858354478 0.40112650987204024 chr7 159138663 13800464 0.0867197432719414 0.947940655305721 chr8 146364022 12536822 0.08565507990754723 1.1605704236679137 chr9 141213431 9948781 0.07045208752133499 0.6202252453024375 chr10 135534747 11623836 0.08576277491409638 0.7061587783960802 chr11 135006516 10855835 0.08040971148385163 0.5036213274513542 chr12 133851895 11051426 0.0825645837886718 0.3540054602387668 chr13 115169878 7862205 0.0682661572325361 0.2966714659079963 chr14 107349540 7336415 0.06834137342367745 0.4151696482504439 chr15 102531392 6589010 0.06426334287941785 0.2933568141516826 chr16 90354753 6753715 0.07474664891176229 0.41957291586305473 chr17 81195210 6305485 0.07765833723442553 0.3691686409422337 chr18 78077248 6107805 0.0782277187843506 1.1251896202922327 chr19 59128983 5027239 0.08502157055534001 1.1737889597720286 chr20 63025520 4736647 0.0751544295072853 0.3391077030063851 chr21 48129895 3017262 0.06268997678054357 0.38545342209509464 chr22 51304566 2614331 0.05095708245539003 0.2675018369992497 chrMT 16571 5588 0.3372156176452839 0.6444238254279568 chrX 155270560 14700380 0.09467589992590997 0.46066720499636493 chrY 59373566 1067038 0.017971600358314337 0.2703316241246194